A microarray is an array of spots of biological or chemical samples (“probes”) immobilized at predefined positions on a substrate. Each spot contains a number of molecules of a single biological or chemical material. To interrogate the array, the microarray is flooded with a fluid containing one or more biological or chemical samples (the “target”), elements of which typically interact with one or more complementary probes on the microarray. In DNA microarrays in particular, the probes are oligonucleotide or cDNA strains, and the target is a fluorescent or radioactive-labeled DNA sample. The molecular strands in the target hybridize with complementary strands in the probe microarray. The hybridized microarray is inspected by a microarray reader, which detects the presence of the radioactive labels or which stimulates the fluorescent labels to emit light through excitation with a laser or other energy sources. The reader detects the position and strength of the label emission in the microarray. Since the probes are placed in predetermined and thus known positions in the microarray, the presence and quantity of target sequences in the fluid are identified by the position at which fluorescence or radiation is detected and the strength of the fluorescence or radiation.
Microarray technology provides an extremely useful tool to conduct biological or chemical experiments in a massive parallel fashion because of the large number of different probes that one can fabricate onto the microarray. It is particularly powerful in screening, profiling and identifying DNA samples.
Microarrays today come as two-dimensional probe matrices fabricated on solid glass or nylon substrates. Because the target samples are generally hard to produce or very expensive, it is highly desirable to perform assays on as many features as possible on a single microarray. This calls for a significant increase in probe density and quantity on a single substrate. In general, microarrays with probe pitch smaller than 500 μm (i.e. density larger than 400 probes per sqr. centimeter) is referred as high density microarrays, otherwise, they are “low density” microarrays.
There are two microarray fabrication techniques on the market, photolithographic and robotic spotting techniques. The photolithographic technique [U.S. Pat. Nos. 5,445,934, 5,744,305] adapts the same fabrication process for electronic integrated circuits to synthesize probes in situ base by base. This technique requires a large capital outlay for equipment running up to hundreds of millions of dollars. The initial setup of new microarray designs is also very expensive due to the high cost of producing photo masks. This technique is therefore only viable in mass production of standard microarrays at a very high volume. Even at high volumes, the complexity in synthesis still limits the production throughput resulting in a high microarray cost. This complexity also limits the length of the synthesized DNA strain to the level of a short oligonucleotide (˜25 bases), which reduces the specificity and sensitivity of hybridization in some applications.
The established robotic spotting technique [U.S. Pat. No. 5,807,522] uses a specially designed mechanical robot, which produces a probe spot on the microarray by dipping a pin head into a fluid containing an off-line synthesized DNA and then spotting it onto the slide at a predetermined position. Washing and drying of the pins are required prior to the spotting of a different probe in the microarray. In current designs of such robotic systems, the spotting pin, and/or the stage carrying the microarray substrates move along the XYZ axes in coordination to deposit samples at controlled positions of the substrates. Because a microarray contains a very large number of different probes, this technique, although highly flexible, is inherently very slow. Even though the speed can be enhanced by employing multiple pin-heads and spotting multiple slides before washing, production throughput remains very low. This technique is therefore not suitable for high volume mass production of microarrays.
In addition to the established quill-pin spotting technologies, there are a number of microarray fabrication techniques that are being developed. These include the inkjet technology and capillary spotting.
Inkjet technology is being deployed to deposit either cDNA/oligonucleotides, or individual nucleotides at defined positions on a substrate to produce an oligonucleotide microarray through in situ synthesis. Consequently, an oligonucleotide is produced in situ one base at a time by delivering monomer-containing solutions onto selected locations, reacting the monomer, rinsing the substrate to remove excess monomers, and drying the substrate to prepare it for the next spot of monomer reactant.
An emerging spotting technique uses capillaries instead of pins to spot DNA probes onto the support. Four references discuss capillary-based spotting techniques for array fabrication:                WO 98/29736, “Multiplexed molecular analysis apparatus and method”, by Genometrix Inc.        WO 00/01859, “Gene pen devices for array printing”, by Orchid Biocomputer Inc.        WO 00/13796, “Capillary printing system”, by Incyte Pharmaceuticals Inc.        WO 99/55461, “Redrawn capillary imaging reservoir”, by Corning Inc.        
In summary, due to the high cost of production, microarrays fabricated with existing technologies are far too expensive as a single use lab supply.